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(-) Description

Title :  CRYSTAL STRUCTURE OF PROCATHEPSIN L1 FROM FASCIOLA HEPATICA
 
Authors :  L. S. Brinen, J. P. Dalton, S. Geiger, R. Marion, C. M. Stack
Date :  08 Dec 06  (Deposition) - 18 Dec 07  (Release) - 09 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase; Thiol Protease; Cysteine Protease; Zymogen, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Stack, C. R. Caffrey, S. M. Donnelly, A. Seshaadri, J. Lowther, J. F. Tort, P. R. Collins, M. W. Robinson, W. Xu, J. H. Mckerrow, C. S. Craik, S. R. Geiger, R. Marion, L. S. Brinen, J. P. Dalton
Structural And Functional Relationships In The Virulence-Associated Cathepsin L Proteases Of The Parasitic Liver Fluke, Fasciola Hepatica.
J. Biol. Chem. V. 283 9896 2008
PubMed-ID: 18160404  |  Reference-DOI: 10.1074/JBC.M708521200

(-) Compounds

Molecule 1 - SECRETED CATHEPSIN L 1
    Chains: A
    EC Number: 3.4.22.15
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: CL1
    Mutation: YES
    Organism Common: LIVER FLUKE
    Organism Scientific: FASCIOLA HEPATICA
    Organism Taxid: 6192
    Other Details: INACTIVE ZYMOGEN FORM
    Strain: IRISH ISOLATE
    Synonym: PROCATHEPSIN L1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2O6X)

(-) Sites  (0, 0)

(no "Site" information available for 2O6X)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:120 -A:163
2A:154 -A:195
3A:253 -A:302

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O6X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O6X)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATLL_FASHE126-137  1A:117-128
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATLL_FASHE267-277  1A:258-268
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATLL_FASHE284-303  1A:275-294
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATLL_FASHE126-137  2A:117-128
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATLL_FASHE267-277  2A:258-268
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATLL_FASHE284-303  2A:275-294

(-) Exons   (0, 0)

(no "Exon" information available for 2O6X)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:306
 aligned with CATLL_FASHE | Q24940 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:310
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
          CATLL_FASHE    17 NDDLWHQWKRMYNKEYNGADDQHRRNIWEKNVKHIQEHNLRHDLGLVTYTLGLNQFTDMTFEEFKAKYLTEMSRASDILSHGVPYEANNRAVPDKIDWRESGYVTEVKDQGNCGSCWAFSTTGTMEGQYMKNERTSISFSEQQLVDCSGPWGNNGCSGGLMENAYQYLKQFGLETESSYPYTAVEGQCRYNKQLGVAKVTGYYTVHSGSEVELKNLVGARRPAAVAVDVESDFMMYRSGIYQSQTCSPLRVNHAVLAVGYGTQGGTDYWIVKNSWGTYWGERGYIRMARNRGNMCGIASLASLPMVARFP 326
               SCOP domains d2o6xa_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2o6xA00 A:8-317 Cysteine proteinases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----Inhibitor_I29-2o6xA02 A:12-71                               ---------------------------Peptidase_C1-2o6xA01 A:99-312                                                                                                                                                                                         ----- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhh....hhhhhh...ee..----.....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhh.hhhhhhhhhh.....................hhhhh.eeeeeeeee...hhhhhhhhhhhhh.eeeee..hhhhhheeeeee...........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ----------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6x A   8 NDDLWHQWKRMYNKEYNGADDQHRRNIWEKNVKHIQEHNLRHDLGLVTYTLGLNQFTDMTFEEFKAKYLTEMSRASDILSHGVPYE----AVPDKIDWRESGYVTEVKDQGNCGSGWAFSTTGTMEGQYMKNERTSISFSEQQLVDCSRPWGNNGCGGGLMENAYQYLKQFGLETESSYPYTAVEGQCRYNKQLGVAKVTGFYTVHSGSEVELKNLVGAEGPAAVAVDVESDFMMYRSGIYQSQTCSPLRVNHAVLAVGYGTQGGTDYWIVKNSWGLSWGERGYIRMVRNRGNMCGIASLASLPMVARFP 317
                                    17        27        37        47        57        67        77        87     |   -|      107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317
                                                                                                                93   98                                                                                                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:306
 aligned with Q7JNQ9_FASHE | Q7JNQ9 from UniProtKB/TrEMBL  Length:326

    Alignment length:310
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
         Q7JNQ9_FASHE    17 NDDLWHQWKRMYNKEYNGADDQHRRNIWEKNVKHIQEHNLRHDLGLVTYTLGLNQFTDMTFEEFKAKYLTEMSRASDILSHGVPYEANNRAVPDKIDWRESGYVTEVKDQGNCGSCWAFSTTGTMEGQYMKNERTSISFSEQQLVDCSRPWGNNGCGGGLMENAYQYLKQFGLETESSYPYTAVEGQCRYNKQLGVAKVTGFYTVHSGSEVELKNLVGAEGPAAVAVDVESDFMMYRSGIYQSQTCSPLRVNHAVLAVGYGTQGGTDYWIVKNSWGLSWGERGYIRMVRNRGNMCGIASLASLPMVARFP 326
               SCOP domains d2o6xa_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2o6xA00 A:8-317 Cysteine proteinases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----Inhibitor_I29-2o6xA02 A:12-71                               ---------------------------Peptidase_C1-2o6xA01 A:99-312                                                                                                                                                                                         ----- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhh....hhhhhh...ee..----.....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhh.hhhhhhhhhh.....................hhhhh.eeeeeeeee...hhhhhhhhhhhhh.eeeee..hhhhhheeeeee...........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6x A   8 NDDLWHQWKRMYNKEYNGADDQHRRNIWEKNVKHIQEHNLRHDLGLVTYTLGLNQFTDMTFEEFKAKYLTEMSRASDILSHGVPYE----AVPDKIDWRESGYVTEVKDQGNCGSGWAFSTTGTMEGQYMKNERTSISFSEQQLVDCSRPWGNNGCGGGLMENAYQYLKQFGLETESSYPYTAVEGQCRYNKQLGVAKVTGFYTVHSGSEVELKNLVGAEGPAAVAVDVESDFMMYRSGIYQSQTCSPLRVNHAVLAVGYGTQGGTDYWIVKNSWGLSWGERGYIRMVRNRGNMCGIASLASLPMVARFP 317
                                    17        27        37        47        57        67        77        87     |   -|      107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317
                                                                                                                93   98
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Peptidase_CA (169)
(-)
Clan: no clan defined [family: Inhibitor_I29] (1)

(-) Gene Ontology  (7, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (CATLL_FASHE | Q24940)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A   (Q7JNQ9_FASHE | Q7JNQ9)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1cjl HUMAN PROCATHEPSIN L